B. Thomas

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Genome‐resolved metagenomics of a bioremediation system for degradation of thiocyanate in mine water containing suspended solid tailings

Brian C. Thomas, J. Banfield, S. Harrison, 2017, MicrobiologyOpen.

Metagenomic analysis with strain-level resolution reveals fine-scale variation in the human pregnancy microbiome

Christine L. Sun, Brian C. Thomas, Daniel B. DiGiulio, 2018, bioRxiv.

Comparative genomics in acid mine drainage biofilm communities reveals metabolic and structural differentiation of co-occurring archaea

Brian C. Thomas, Cindy J. Castelle, J. Banfield, 2013, BMC Genomics.

Following tetraploidy in an Arabidopsis ancestor, genes were removed preferentially from one homeolog leaving clusters enriched in dose-sensitive genes.

Brian C. Thomas, Michael Freeling, Brian C Thomas, 2006, Genome research.

Arabidopsis intragenomic conserved noncoding sequence

Brian C. Thomas, M. Freeling, E. Lyons, 2007, Proceedings of the National Academy of Sciences.

Identical bacterial populations colonize premature infant gut, skin, and oral microbiomes and exhibit different in situ growth rates.

Brian C. Thomas, D. Burstein, J. Banfield, 2017, Genome Research.

Measurement of bacterial replication rates in microbial communities

Brian C. Thomas, J. Banfield, C. Brown, 2016, Nature Biotechnology.

In Situ Replication Rates for Uncultivated Bacteria in Microbial Communities

J. Banfield, C. Brown, Matthew R. Olm, 2016, bioRxiv.

Metagenomic reconstructions of bacterial CRISPR loci constrain population histories

Christine L. Sun, Rodolphe Barrangou, Jillian F Banfield, 2015, The ISME Journal.

Strong bias in the bacterial CRISPR elements that confer immunity to phage

Christine L. Sun, Rodolphe Barrangou, Jillian F Banfield, 2013, Nature Communications.

Phage mutations in response to CRISPR diversification in a bacterial population.

Christine L. Sun, Philippe Horvath, Rodolphe Barrangou, 2013, Environmental microbiology.

New CRISPR-Cas systems from uncultivated microbes

Jennifer A. Doudna, David Burstein, Brian C. Thomas, 2016, Nature.

Major bacterial lineages are essentially devoid of CRISPR-Cas viral defence systems

Christine L. Sun, Alexander J Probst, Alexander J. Probst, 2016, Nature Communications.

Virus-Host and CRISPR Dynamics in Archaea-Dominated Hypersaline Lake Tyrrell, Victoria, Australia

J. Banfield, E. Allen, J. Emerson, 2013, Archaea.

Novel Type V-A CRISPR Effectors Are Active Nucleases with Expanded Targeting Capabilities

C. Brown, Cristina N Butterfield, Audra E. Devoto, 2020, The CRISPR journal.

CRISPR Immunity Drives Rapid Phage Genome Evolution in Streptococcus thermophilus

Brian C. Thomas, Rodolphe Barrangou, Jillian F. Banfield, 2015, mBio.

Microbes in the neonatal intensive care unit resemble those found in the gut of premature infants

Brian C. Thomas, Christopher S. Miller, Jillian F Banfield, 2014, Microbiome.

Differential gene expression and the importance of regulatory ncRNAs in acidophilic microorganisms

J. Banfield, L. Hauser, Mauna Dasari, 2019, bioRxiv.

The human gut and groundwater harbor non-photosynthetic bacteria belonging to a new candidate phylum sibling to Cyanobacteria

Brian C. Thomas, Laura A Hug, Omry Koren, 2013, eLife.

Megaphages infect Prevotella and variants are widespread in gut microbiomes

Brian C. Thomas, J. Banfield, F. Aarestrup, 2018, bioRxiv.

The developing premature infant gut microbiome is a major factor shaping the microbiome of neonatal intensive care unit rooms

J. Banfield, B. Firek, M. Morowitz, 2018, bioRxiv.

Thousands of microbial genomes shed light on interconnected biogeochemical processes in an aquifer system

Brian C. Thomas, Eoin L. Brodie, Alexander J. Probst, 2016, Nature Communications.

EMIRGE: reconstruction of full-length ribosomal genes from microbial community short read sequencing data

Brian C. Thomas, Christopher S. Miller, J. Banfield, 2011, Genome Biology.

Evidence for persistent and shared bacterial strains against a background of largely unique gut colonization in hospitalized premature infants

Brian C. Thomas, Itai Sharon, J. Banfield, 2016, The ISME Journal.

Unusual biology across a group comprising more than 15% of domain Bacteria

Brian C. Thomas, Itai Sharon, L. Hug, 2015, Nature.

Gut bacteria are rarely shared by co-hospitalized premature infants, regardless of necrotizing enterocolitis development

Brian C. Thomas, Itai Sharon, Cindy J. Castelle, 2015, eLife.

Time series community genomics analysis reveals rapid shifts in bacterial species, strains, and phage during infant gut colonization

Brian C. Thomas, Itai Sharon, J. Banfield, 2013, Genome research.

Recovery of genomes from metagenomes via a dereplication, aggregation and scoring strategy

Alexander J Probst, Alexander J. Probst, Jillian F Banfield, 2017, Nature Microbiology.

Gene structure and minimal promoter of mouse rdh1.

M. Zhang, J. L. Napoli, B. Thomas, 2003, Gene.

Genome-Resolved Metagenomics and Detailed Geochemical Speciation Analyses Yield New Insights into Microbial Mercury Cycling in Geothermal Springs

J. Banfield, K. Holt, R. Wick, 2020, Applied and Environmental Microbiology.

Bioreactor microbial ecosystems for thiocyanate and cyanide degradation unravelled with genome-resolved metagenomics.

J. Banfield, S. Harrison, R. Kantor, 2015, Environmental microbiology.

A new view of the tree of life

Brian C. Thomas, Alexander J. Probst, L. Hug, 2016, Nature Microbiology.

New Approaches Indicate Constant Viral Diversity despite Shifts in Assemblage Structure in an Australian Hypersaline Lake

Brian C. Thomas, Jillian F. Banfield, Karla B. Heidelberg, 2013, Applied and Environmental Microbiology.

Strain-resolved analysis of hospital rooms and infants reveals overlap between the human and room microbiome

J. Banfield, B. Firek, M. Morowitz, 2017, Nature Communications.

Proteogenomic basis for ecological divergence of closely related bacteria in natural acidophilic microbial communities

Vincent J. Denef, Paul Wilmes, Ryan S. Mueller, 2010, Proceedings of the National Academy of Sciences.

Mediterranean grassland soil C–N compound turnover is dependent on rainfall and depth, and is mediated by genomically divergent microorganisms

Brian C. Thomas, D. Burstein, J. Banfield, 2019, Nature Microbiology.

Processing of grassland soil C-N compounds into soluble and volatile molecules is depth stratified and mediated by genomically novel bacteria and archaea

D. Burstein, J. Banfield, Karthik Anantharaman, 2018, bioRxiv.

Accurate, multi-kb reads resolve complex populations and detect rare microorganisms

Brian C. Thomas, Dmitry Pushkarev, T. Blauwkamp, 2015, Genome research.

Novel soil bacteria possess diverse genes for secondary metabolite biosynthesis

Brian C. Thomas, Jillian F. Banfield, Alexander Crits-Christoph, 2018, Nature.

Biology of a widespread uncultivated archaeon that contributes to carbon fixation in the subsurface

Brian C. Thomas, Alexander J. Probst, Anna K. Auerbach, 2014, Nature Communications.

Strain-resolved analysis of hospital rooms and infants reveals overlap between the human and room microbiome

Jillian F Banfield, Brian C Thomas, J. Banfield, 2017, Nature Communications.

G-Boxes, Bigfoot Genes, and Environmental Response: Characterization of Intragenomic Conserved Noncoding Sequences in Arabidopsis[W]

Brian C. Thomas, M. Freeling, E. Lyons, 2007, The Plant Cell Online.

Short-Read Assembly of Full-Length 16S Amplicons Reveals Bacterial Diversity in Subsurface Sediments

Kelly C. Wrighton, Brian C. Thomas, Jillian F. Banfield, 2013, PloS one.

Gene-balanced duplications, like tetraploidy, provide predictable drive to increase morphological complexity.

Brian C. Thomas, M. Freeling, B. Thomas, 2006, Genome research.

Genome-Resolved Metagenomic Analysis Reveals Roles for Candidate Phyla and Other Microbial Community Members in Biogeochemical Transformations in Oil Reservoirs

Brian C. Thomas, Jillian F. Banfield, Gary L. Andersen, 2016, mBio.

Genome-reconstruction for eukaryotes from complex natural microbial communities

Brian C. Thomas, Alexander J. Probst, J. Banfield, 2017, bioRxiv.

Expanded diversity of microbial groups that shape the dissimilatory sulfur cycle

Brian C. Thomas, J. Banfield, Karthik Anantharaman, 2018, The ISME Journal.

Proteogenomic analyses indicate bacterial methylotrophy and archaeal heterotrophy are prevalent below the grass root zone

Brian C. Thomas, Alexander J. Probst, S. Tringe, 2016, PeerJ.

Community-wide analysis of microbial genome sequence signatures

Brian C. Thomas, Anders F. Andersson, J. Banfield, 2009, Genome Biology.

Hydrogen-based metabolism as an ancestral trait in lineages sibling to the Cyanobacteria

Itai Sharon, Cindy J. Castelle, D. Burstein, 2019, Nature Communications.

Supplemental Figures Supplemental Figure 1 -esom Showing Best Blast Hit of Scaffolds

Brian C. Thomas, Itai Sharon, Cindy J. Castelle, 2022 .

A Semi-Quantitative, Synteny-Based Method to Improve Functional Predictions for Hypothetical and Poorly Annotated Bacterial and Archaeal Genes

Adam Zemla, Brian C. Thomas, Jillian F. Banfield, 2011, PLoS Comput. Biol..

Proteome changes in the initial bacterial colonist during ecological succession in an acid mine drainage biofilm community.

Brian C. Thomas, Chongle Pan, Ryan S. Mueller, 2011, Environmental microbiology.

Strain-resolved community genomic analysis of gut microbial colonization in a premature infant

Vincent J. Denef, Brian C. Thomas, Jillian F Banfield, 2010, Proceedings of the National Academy of Sciences.

Microbial communities across a hillslope‐riparian transect shaped by proximity to the stream, groundwater table, and weathered bedrock

K. Williams, J. Banfield, S. Hubbard, 2018, bioRxiv.

Genomic Expansion of Domain Archaea Highlights Roles for Organisms from New Phyla in Anaerobic Carbon Cycling

Kenneth H. Williams, Susannah G. Tringe, Kelly C. Wrighton, 2015, Current Biology.

Diverse uncultivated ultra-small bacterial cells in groundwater

Brian C. Thomas, S. Tringe, K. Williams, 2015, Nature Communications.

Dynamic Viral Populations in Hypersaline Systems as Revealed by Metagenomic Assembly

Brian C. Thomas, J. Banfield, E. Allen, 2012, Applied and Environmental Microbiology.

RubisCO of a nucleoside pathway known from Archaea is found in diverse uncultivated phyla in bacteria

Brian C. Thomas, Itai Sharon, Cindy J. Castelle, 2016, The ISME Journal.

Extraordinary phylogenetic diversity and metabolic versatility in aquifer sediment

Kenneth H. Williams, Jonathan A. Eisen, Susannah G. Tringe, 2013, Nature Communications.

Fermentation, Hydrogen, and Sulfur Metabolism in Multiple Uncultivated Bacterial Phyla

Brian C. Thomas, Christopher S. Miller, Itai Sharon, 2012, Science.

Metagenomic and lipid analyses reveal a diel cycle in a hypersaline microbial ecosystem

Alexander J. Probst, L. Hug, J. Banfield, 2015, The ISME Journal.

Metabolome-Proteome Differentiation Coupled to Microbial Divergence

Vincent J. Denef, Brian C. Thomas, Ryan S. Mueller, 2010, mBio.

Ecological distribution and population physiology defined by proteomics in a natural microbial community

Vincent J. Denef, Ryan S. Mueller, Richard L. Smith, 2010, Molecular systems biology.

Heterotrophic Archaea Contribute to Carbon Cycling in Low-pH, Suboxic Biofilm Communities

Christine L. Sun, Brian C. Thomas, Ryan S. Mueller, 2012, Applied and Environmental Microbiology.

Persisting Viral Sequences Shape Microbial CRISPR-based Immunity

Wayne M. Getz, Ariel D. Weinberger, Christine L. Sun, 2012, PLoS Comput. Biol..

The Source and Evolutionary History of a Microbial Contaminant Identified Through Soil Metagenomic Analysis

Brian C. Thomas, J. Banfield, Cristina N Butterfield, 2017, mBio.

Development of a Knowledgebase to Integrate, Analyze, Distribute, and Visualize Microbial Community Systems Biology Data

Jillian F. Banfield, Brian Thomas, J. Banfield, 2015 .

Community genomic analyses constrain the distribution of metabolic traits across the Chloroflexi phylum and indicate roles in sediment carbon cycling

Brian C. Thomas, Itai Sharon, L. Hug, 2013, Microbiome.

Hospitalized Premature Infants Are Colonized by Related Bacterial Strains with Distinct Proteomic Profiles

Brian C. Thomas, Jillian F. Banfield, Robert L. Hettich, 2017, mBio.

Conserved noncoding sequences in the grasses.

A. Bashir, S. Goff, M. Freeling, 2003, Genome research.

Genomic resolution of a cold subsurface aquifer community provides metabolic insights for novel microbes adapted to high CO2 concentrations

Brian C. Thomas, Alexander J. Probst, Itai Sharon, 2017, Environmental microbiology.

Metagenomic analysis of a high carbon dioxide subsurface microbial community populated by chemolithoautotrophs and bacteria and archaea from candidate phyla.

Brian C. Thomas, J. Banfield, J. Emerson, 2016, Environmental microbiology.

Aquifer environment selects for microbial species cohorts in sediment and groundwater

L. Hug, S. Tringe, K. Williams, 2015, The ISME Journal.

Compact Cas9d and HEARO enzymes for genome editing discovered from uncultivated microbes

C. Brown, Cristina N Butterfield, G. Cost, 2022, Nature communications.

Genome-Resolved Meta-Omics Ties Microbial Dynamics to Process Performance in Biotechnology for Thiocyanate Degradation.

Brian C. Thomas, S. Tringe, J. Banfield, 2017, Environmental science & technology.

Retroelement guided protein diversification abounds in vast lineages of bacteria and archaea

Brian C. Thomas, Cindy J. Castelle, D. Burstein, 2017, Nature Microbiology.

COMPARISON OF PROTEIN AND MRNA PROFILES OF ESCHERICHIA COLI : DATA VISUALIZATION AND ANALYSIS OF SPECIFIC GENE GROUPS

M. Platt, S. Kustu, Feng Yang, 2006 .

Differential depth distribution of microbial function and putative symbionts through sediment-hosted aquifers in the deep terrestrial subsurface

Alexander J. Probst, J. Banfield, M. Stieglmeier, 2018, Nature Microbiology.

Unusual respiratory capacity and nitrogen metabolism in a Parcubacterium (OD1) of the Candidate Phyla Radiation

Cindy J. Castelle, K. Williams, J. Banfield, 2017, Scientific Reports.

Critical biogeochemical functions in the subsurface are associated with bacteria from new phyla and little studied lineages.

Brian C. Thomas, Itai Sharon, L. Hug, 2016, Environmental microbiology.

Small Genomes and Sparse Metabolisms of Sediment-Associated Bacteria from Four Candidate Phyla

Brian C. Thomas, Itai Sharon, L. Hug, 2013, mBio.

Novel Microbial Diversity and Functional Potential in the Marine Mammal Oral Microbiome

Christine L. Sun, D. Burstein, J. Banfield, 2017, Current Biology.

Recovery of genomes from metagenomes via a dereplication, aggregation and scoring strategy

Brian C. Thomas, Alexander J. Probst, S. Tringe, 2017, Nature Microbiology.

Differential depth distribution of microbial function and putative symbionts through sediment-hosted aquifers in the deep terrestrial subsurface

Alexander J. Probst, J. Banfield, M. Stieglmeier, 2018, Nature Microbiology.

Potential for microbial H2 and metal transformations associated with novel bacteria and archaea in deep terrestrial subsurface sediments

Yuki Amano, Alexander J. Probst, Karthik Anantharaman, 2017, The ISME Journal.

Elevated temperature alters proteomic responses of individual organisms within a biofilm community

Annika C. Mosier, J. Banfield, R. Hettich, 2014, The ISME Journal.

Metabolic interdependencies between phylogenetically novel fermenters and respiratory organisms in an unconfined aquifer

Itai Sharon, L. Hug, Cindy J. Castelle, 2014, The ISME Journal.

Comparison of environmental and isolate Sulfobacillus genomes reveals diverse carbon, sulfur, nitrogen, and hydrogen metabolisms

J. Banfield, C. Brown, N. Justice, 2014, BMC Genomics.

Metabolites Associated with Adaptation of Microorganisms to an Acidophilic, Metal-Rich Environment Identified by Stable-Isotope-Enabled Metabolomics

Brian C. Thomas, Annika C. Mosier, J. Banfield, 2013, mBio.

Comparison of environmental and isolate Sulfobacillus genomes reveals diverse carbon, sulfur, nitrogen, and hydrogen metabolisms

J. Banfield, C. Brown, N. Justice, 2014, BMC Genomics.

Title Genome resolved analysis of a premature infant gut microbial community reveals a Varibaculum cambriense genome and a shift towards fermentation-based metabolism during the third week of life Permalink

Itai Sharon, Cindy J. Castelle, J. Banfield, 2013 .

Temporal and Spatial Expression of Arabidopsis Gene Homologs Control Daylength Adaptation and Bulb Formation in Onion (Allium cepa L.)

Brian C. Thomas, Md. Harun Ar Rashid, Wei Cheng, 2019, Scientific Reports.

A Subunit Interaction in Chloroplast ATP Synthase Determined by Genetic Complementation between Chloroplast and Bacterial ATP Synthase Genes (*)

Zugen Chen, M. Richter, P. Gegenheimer, 1995, The Journal of Biological Chemistry.

Subsurface carbon monoxide oxidation capacity revealed through genome-resolved metagenomics of a carboxydotroph

Brian C. Thomas, J. Banfield, A. Mu, 2020, bioRxiv.

Structure in an Australian Hypersaline Lake Diversity despite Shifts in Assemblage New Approaches Indicate Constant Viral

J. Banfield, J. Emerson, K. Heidelberg, 2014 .

Dramatic expansion of microbial groups that shape the global sulfur cycle

J. Banfield, Karthik Anantharaman, S. Jungbluth, 2017, bioRxiv.

Lawrence Berkeley National Laboratory Recent Work Title RubisCO of a nucleoside pathway known from Archaea is found in diverse uncultivated phyla in bacteria Permalink

Itai Sharon, Cindy J. Castelle, K. Williams, 2016 .

Complete 4.55-Megabase-Pair Genome of “Candidatus Fluviicola riflensis,” Curated from Short-Read Metagenomic Sequences

Brian C. Thomas, K. Williams, J. Banfield, 2017, Genome Announcements.

Analysis of five complete genome sequences for members of the class Peribacteria in the recently recognized Peregrinibacteria bacterial phylum

Alexander J. Probst, Cindy J. Castelle, D. Burstein, 2016, PeerJ.

Ecological and genomic profiling of anaerobic methane-oxidizing archaea in a deep granitic environment

J. Banfield, Alex W Hernsdorf, Yohey Suzuki, 2017, The ISME Journal.

Disturbed subsurface microbial communities follow equivalent trajectories despite different structural starting points.

K. Williams, J. Banfield, J. Gilbert, 2015, Environmental microbiology.

Biostimulation induces syntrophic interactions that impact C, S and N cycling in a sediment microbial community

Brian C. Thomas, Christopher S. Miller, Itai Sharon, 2012, The ISME Journal.

New Group in the Leptospirillum Clade: Cultivation-Independent Community Genomics, Proteomics, and Transcriptomics of the New Species “Leptospirillum Group IV UBA BS”

J. Banfield, R. Hettich, M. Shah, 2013, Applied and Environmental Microbiology.

Community transcriptomics reveals unexpected high microbial diversity in acidophilic biofilm communities

J. Banfield, L. Comolli, D. Goltsman, 2014, The ISME Journal.

Proteogenomic Monitoring of Geobacter Physiology during Stimulated Uranium Bioremediation

Kenneth H. Williams, Brian C. Thomas, Jillian F. Banfield, 2009, Applied and Environmental Microbiology.

Microbial Community Structure and the Persistence of Cyanobacterial Populations in Salt Crusts of the Hyperarid Atacama Desert from Genome-Resolved Metagenomics

Alexander J. Probst, J. Banfield, K. Finstad, 2017, Front. Microbiol..

Hydrogen-based metabolism as an ancestral trait in lineages sibling to the Cyanobacteria

Itai Sharon, D. Burstein, J. Banfield, 2018, bioRxiv.

A novel Chromatiales bacterium is a potential sulfide oxidizer in multiple orders of marine sponges

Brian C. Thomas, J. Banfield, L. Alvarez-Cohen, 2018, Environmental microbiology.

Novel and Engineered Type II CRISPR Systems from Uncultivated Microbes with Broad Genome Editing Capability

C. Brown, Cristina N Butterfield, G. Cost, 2023, The CRISPR journal.

Novel CRISPR-Associated Gene-Editing Systems Discovered in Metagenomic Samples Enable Efficient and Specific Genome Engineering

C. Brown, Cristina N Butterfield, G. Cost, 2021, The CRISPR journal.

Biological Systems Research on the Role of Microbial Communities in Carbon Cycling 112 Approaches to Systematically Examine Carbon Flux in Microbial Communities Using ‘ Omics ’ and Stable Isotope Probing

R. Hettich, S. Singer, T. Northen, 2012 .

Thousands of microbial genomes shed light on interconnected biogeochemical processes in an aquifer system

Eoin L. Brodie, Alexander J. Probst, Itai Sharon, 2016, Nature Communications.